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sanger-pathogens / Artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation
http://sanger-pathogens.github.io/Artemis
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installation with mvn #303

Closed lalalagartija closed 4 years ago

lalalagartija commented 4 years ago

Hi, I did not manage to install Artemis with mvn Do you know why I get this error ?

`bla@linne:~/Software/Artemis$ mvn -e clean package [INFO] Error stacktraces are turned on. [INFO] Scanning for projects... [INFO] [INFO] ------------------------< uk.ac.sanger:artemis >------------------------ [INFO] Building Artemis 18.1.0 [INFO] --------------------------------[ jar ]--------------------------------- [INFO] [INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ artemis --- [INFO] Deleting /home/rigou/Software/Artemis/target [INFO] [INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-maven-3) @ artemis --- [INFO] [INFO] --- maven-install-plugin:2.5.2:install-file (install-biojava-jar) @ artemis --- [INFO] pom.xml not found in biojava.jar [INFO] Installing /home/rigou/Software/Artemis/lib/biojava.jar to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.jar [INFO] Installing /tmp/mvninstall8209771311433696208.pom to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.pom [INFO] [INFO] --- maven-install-plugin:2.5.2:install-file (install-jemalign-jar) @ artemis --- [INFO] pom.xml not found in jemAlign.jar [INFO] Installing /home/rigou/Software/Artemis/lib/jemAlign.jar to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.jar [INFO] Installing /tmp/mvninstall2291838399772923129.pom to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.pom [INFO] [INFO] --- maven-install-plugin:2.5.2:install-file (install-j2ssh-core-jar) @ artemis --- [INFO] pom.xml not found in j2ssh-core.jar [INFO] Installing /home/rigou/Software/Artemis/lib/j2ssh-core.jar to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.jar [INFO] Installing /tmp/mvninstall94387948769839764.pom to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.pom [INFO] [INFO] --- maven-install-plugin:2.5.2:install-file (install-ibatis-jar) @ artemis --- [INFO] pom.xml not found in ibatis-2.3.4.726.jar [INFO] Installing /home/rigou/Software/Artemis/lib/ibatis-2.3.4.726.jar to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.jar [INFO] Installing /tmp/mvninstall5370814239589167909.pom to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.pom [INFO] [INFO] --- properties-maven-plugin:1.0.0:read-project-properties (load-external-properties) @ artemis --- [INFO] Quiet processing - ignoring properties cannot be loaded from File: /home/rigou/Software/Artemis/maven.properties [INFO] [INFO] --- maven-antrun-plugin:1.8:run (updating-software-version-number) @ artemis --- [INFO] Executing tasks

main: [INFO] Executed tasks [INFO] [INFO] --- jacoco-maven-plugin:0.8.2:prepare-agent (pre-unit-test) @ artemis --- [INFO] Skipping JaCoCo execution because property jacoco.skip is set. [INFO] [INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ artemis --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 35 resources [INFO] [INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-property-files) @ artemis --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 37 resources [INFO] [INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-icons-folder) @ artemis --- [INFO] Using 'UTF-8' encoding to copy filtered resources. [INFO] Copying 5 resources [INFO] [INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ artemis --- [INFO] Changes detected - recompiling the module! [INFO] Compiling 585 source files to /home/rigou/Software/Artemis/target/classes [INFO] ------------------------------------------------------------------------ [INFO] BUILD FAILURE [INFO] ------------------------------------------------------------------------ [INFO] Total time: 2.827 s [INFO] Finished at: 2020-01-30T17:34:03+01:00 [INFO] ------------------------------------------------------------------------ [ERROR] Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project artemis: Fatal error compiling: invalid flag: --release -> [Help 1] org.apache.maven.lifecycle.LifecycleExecutionException: Failed to execute goal org.apache.maven.plugins:maven-compiler-plugin:3.8.0:compile (default-compile) on project artemis: Fatal error compiling at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:215) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288) at org.apache.maven.cli.MavenCli.main (MavenCli.java:192) at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke (Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347) Caused by: org.apache.maven.plugin.MojoExecutionException: Fatal error compiling at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1140) at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288) at org.apache.maven.cli.MavenCli.main (MavenCli.java:192) at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke (Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347) Caused by: org.codehaus.plexus.compiler.CompilerException: invalid flag: --release at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:173) at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174) at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1129) at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288) at org.apache.maven.cli.MavenCli.main (MavenCli.java:192) at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke (Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347) Caused by: java.lang.IllegalArgumentException: invalid flag: --release at com.sun.tools.javac.api.JavacTool.processOptions (JavacTool.java:206) at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:156) at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:107) at com.sun.tools.javac.api.JavacTool.getTask (JavacTool.java:64) at org.codehaus.plexus.compiler.javac.JavaxToolsCompiler.compileInProcess (JavaxToolsCompiler.java:125) at org.codehaus.plexus.compiler.javac.JavacCompiler.performCompile (JavacCompiler.java:174) at org.apache.maven.plugin.compiler.AbstractCompilerMojo.execute (AbstractCompilerMojo.java:1129) at org.apache.maven.plugin.compiler.CompilerMojo.execute (CompilerMojo.java:188) at org.apache.maven.plugin.DefaultBuildPluginManager.executeMojo (DefaultBuildPluginManager.java:137) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:210) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:156) at org.apache.maven.lifecycle.internal.MojoExecutor.execute (MojoExecutor.java:148) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:117) at org.apache.maven.lifecycle.internal.LifecycleModuleBuilder.buildProject (LifecycleModuleBuilder.java:81) at org.apache.maven.lifecycle.internal.builder.singlethreaded.SingleThreadedBuilder.build (SingleThreadedBuilder.java:56) at org.apache.maven.lifecycle.internal.LifecycleStarter.execute (LifecycleStarter.java:128) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:305) at org.apache.maven.DefaultMaven.doExecute (DefaultMaven.java:192) at org.apache.maven.DefaultMaven.execute (DefaultMaven.java:105) at org.apache.maven.cli.MavenCli.execute (MavenCli.java:956) at org.apache.maven.cli.MavenCli.doMain (MavenCli.java:288) at org.apache.maven.cli.MavenCli.main (MavenCli.java:192) at sun.reflect.NativeMethodAccessorImpl.invoke0 (Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke (NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke (DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke (Method.java:498) at org.codehaus.plexus.classworlds.launcher.Launcher.launchEnhanced (Launcher.java:282) at org.codehaus.plexus.classworlds.launcher.Launcher.launch (Launcher.java:225) at org.codehaus.plexus.classworlds.launcher.Launcher.mainWithExitCode (Launcher.java:406) at org.codehaus.plexus.classworlds.launcher.Launcher.main (Launcher.java:347) [ERROR] [ERROR] Re-run Maven using the -X switch to enable full debug logging. [ERROR] [ERROR] For more information about the errors and possible solutions, please read the following articles: [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/MojoExecutionException `

Thank you !

kpepper commented 4 years ago

Hi @lalalagartija. Please see the resolution for issue #302 - looks like you are using the wrong Java version. Build steps are detailed in the README.

lalalagartija commented 4 years ago

Thank you very much. I was indead using the wrong java version. Now I have openjdk-11 and still get the error when I removed and downloaded again artemis : 

WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.google.inject.internal.cglib.core.$ReflectUtils$1 (file:/usr/share/maven/lib/guice.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of com.google.inject.internal.cglib.core.$ReflectUtils$1
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
[INFO] Scanning for projects...
[INFO] 
[INFO] ------------------------< uk.ac.sanger:artemis >------------------------
[INFO] Building Artemis 18.1.0
[INFO] --------------------------------[ jar ]---------------------------------
[INFO] 
[INFO] --- maven-clean-plugin:2.5:clean (default-clean) @ artemis ---
[INFO] 
[INFO] --- maven-enforcer-plugin:1.4.1:enforce (enforce-maven-3) @ artemis ---
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install-file (install-biojava-jar) @ artemis ---
[INFO] pom.xml not found in biojava.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/biojava.jar to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.jar
[INFO] Installing /tmp/mvninstall22371457389316888.pom to /home/rigou/.m2/repository/org/biojava/biojava/1.6/biojava-1.6.pom
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install-file (install-jemalign-jar) @ artemis ---
[INFO] pom.xml not found in jemAlign.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/jemAlign.jar to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.jar
[INFO] Installing /tmp/mvninstall6625045835183953792.pom to /home/rigou/.m2/repository/org/emboss/jemboss/1.0/jemboss-1.0.pom
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install-file (install-j2ssh-core-jar) @ artemis ---
[INFO] pom.xml not found in j2ssh-core.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/j2ssh-core.jar to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.jar
[INFO] Installing /tmp/mvninstall9533148296565218020.pom to /home/rigou/.m2/repository/com/sshtools/j2ssh-core/0.2.9/j2ssh-core-0.2.9.pom
[INFO] 
[INFO] --- maven-install-plugin:2.5.2:install-file (install-ibatis-jar) @ artemis ---
[INFO] pom.xml not found in ibatis-2.3.4.726.jar
[INFO] Installing /home/rigou/Software/Artemis/lib/ibatis-2.3.4.726.jar to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.jar
[INFO] Installing /tmp/mvninstall13795943866877277802.pom to /home/rigou/.m2/repository/com/ibatis/ibatis/2.3.4.726/ibatis-2.3.4.726.pom
[INFO] 
[INFO] --- properties-maven-plugin:1.0.0:read-project-properties (load-external-properties) @ artemis ---
[INFO] Quiet processing - ignoring properties cannot be loaded from File: /home/rigou/Software/Artemis/maven.properties
[INFO] 
[INFO] --- maven-antrun-plugin:1.8:run (updating-software-version-number) @ artemis ---
[INFO] Executing tasks

main:
[INFO] Executed tasks
[INFO] 
[INFO] --- jacoco-maven-plugin:0.8.2:prepare-agent (pre-unit-test) @ artemis ---
[INFO] Skipping JaCoCo execution because property jacoco.skip is set.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:resources (default-resources) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 35 resources
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-property-files) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 37 resources
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:copy-resources (copy-icons-folder) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 5 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:compile (default-compile) @ artemis ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 585 source files to /home/rigou/Software/Artemis/target/classes
[WARNING] /home/rigou/Software/Artemis/src/main/java/uk/ac/sanger/artemis/j2ssh/SshFileManager.java:[437,17] destroy() in java.lang.Thread has been deprecated and marked for removal
[INFO] /home/rigou/Software/Artemis/src/main/java/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: Some input files use or override a deprecated API.
[INFO] /home/rigou/Software/Artemis/src/main/java/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/rigou/Software/Artemis/src/main/java/uk/ac/sanger/artemis/components/filetree/SshJTreeTable.java: Some input files use unchecked or unsafe operations.
[INFO] /home/rigou/Software/Artemis/src/main/java/uk/ac/sanger/artemis/components/filetree/SshJTreeTable.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- build-helper-maven-plugin:3.0.0:add-test-source (add-test-source) @ artemis ---
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-annotations/1.5.4/plexus-component-annotations-1.5.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-component-annotations/1.5.4/plexus-component-annotations-1.5.4.pom (815 B at 1.6 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.5.4/plexus-containers-1.5.4.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-containers/1.5.4/plexus-containers-1.5.4.pom (4.2 kB at 60 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.5/plexus-2.0.5.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus/2.0.5/plexus-2.0.5.pom (17 kB at 170 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.pom (4.7 kB at 66 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/22/maven-shared-components-22.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-components/22/maven-shared-components-22.pom (5.1 kB at 68 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/27/maven-parent-27.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-parent/27/maven-parent-27.pom (41 kB at 345 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/apache/17/apache-17.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/apache/17/apache-17.pom (16 kB at 176 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/3.0.0/maven-shared-io-3.0.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/3.0.0/maven-shared-io-3.0.0.pom (4.2 kB at 49 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-compat/3.0/maven-compat-3.0.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-compat/3.0/maven-compat-3.0.pom (4.0 kB at 46 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0-beta-6/wagon-provider-api-1.0-beta-6.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/1.0-beta-6/wagon-provider-api-1.0-beta-6.pom (1.8 kB at 16 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon/1.0-beta-6/wagon-1.0-beta-6.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon/1.0-beta-6/wagon-1.0-beta-6.pom (12 kB at 87 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.2/plexus-utils-1.4.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.4.2/plexus-utils-1.4.2.pom (2.0 kB at 16 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/2.10/wagon-provider-api-2.10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/2.10/wagon-provider-api-2.10.pom (1.7 kB at 20 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon/2.10/wagon-2.10.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon/2.10/wagon-2.10.pom (21 kB at 281 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/3.0.0/maven-shared-io-3.0.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-compat/3.0/maven-compat-3.0.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/2.10/wagon-provider-api-2.10.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/file-management/3.0.0/file-management-3.0.0.jar (35 kB at 336 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/shared/maven-shared-io/3.0.0/maven-shared-io-3.0.0.jar (41 kB at 307 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/wagon/wagon-provider-api/2.10/wagon-provider-api-2.10.jar (54 kB at 421 kB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-compat/3.0/maven-compat-3.0.jar (285 kB at 850 kB/s)
[INFO] Test Source directory: /home/rigou/Software/Artemis/src/test/evosuite added.
[INFO] 
[INFO] --- maven-resources-plugin:3.0.2:testResources (default-testResources) @ artemis ---
[INFO] Using 'UTF-8' encoding to copy filtered resources.
[INFO] Copying 60 resources
[INFO] 
[INFO] --- maven-compiler-plugin:3.8.0:testCompile (default-testCompile) @ artemis ---
[INFO] Changes detected - recompiling the module!
[INFO] Compiling 855 source files to /home/rigou/Software/Artemis/target/test-classes
[WARNING] /home/rigou/Software/Artemis/src/test/evosuite/uk/ac/sanger/artemis/components/RunPfamSearchThread_ESTest.java:[35,43] countStackFrames() in java.lang.Thread has been deprecated and marked for removal
[WARNING] /home/rigou/Software/Artemis/src/test/evosuite/uk/ac/sanger/artemis/components/RunPfamSearchThread_ESTest.java:[42,43] countStackFrames() in java.lang.Thread has been deprecated and marked for removal
[WARNING] /home/rigou/Software/Artemis/src/test/evosuite/uk/ac/sanger/artemis/components/ProgressThread_ESTest.java:[28,38] countStackFrames() in java.lang.Thread has been deprecated and marked for removal
[INFO] /home/rigou/Software/Artemis/src/test/evosuite/uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry_ESTest.java: Some input files use or override a deprecated API.
[INFO] /home/rigou/Software/Artemis/src/test/evosuite/uk/ac/sanger/artemis/io/MSPcrunchDocumentEntry_ESTest.java: Recompile with -Xlint:deprecation for details.
[INFO] /home/rigou/Software/Artemis/src/test/java/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java: Some input files use unchecked or unsafe operations.
[INFO] /home/rigou/Software/Artemis/src/test/java/uk/ac/sanger/artemis/components/TransferAnnotationToolTest.java: Recompile with -Xlint:unchecked for details.
[INFO] 
[INFO] --- maven-surefire-plugin:2.22.1:test (default-test) @ artemis ---
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/2.22.1/maven-surefire-common-2.22.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/2.22.1/maven-surefire-common-2.22.1.pom (11 kB at 176 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.5.2/maven-plugin-annotations-3.5.2.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.5.2/maven-plugin-annotations-3.5.2.pom (1.6 kB at 31 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-tools/3.5.2/maven-plugin-tools-3.5.2.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/2.22.1/surefire-api-2.22.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/2.22.1/surefire-api-2.22.1.pom (3.5 kB at 63 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/2.22.1/surefire-logger-api-2.22.1.pom
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/2.22.1/surefire-booter-2.22.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/2.22.1/surefire-booter-2.22.1.pom (7.5 kB at 138 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/2.2.1/maven-toolchain-2.2.1.pom
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/2.2.1/maven-toolchain-2.2.1.pom (3.3 kB at 61 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M8/qdox-2.0-M8.pom
Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M8/qdox-2.0-M8.pom (16 kB at 273 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/2.22.1/maven-surefire-common-2.22.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-api/2.22.1/surefire-api-2.22.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.5.2/maven-plugin-annotations-3.5.2.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/2.22.1/surefire-logger-api-2.22.1.jar
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-booter/2.22.1/surefire-booter-2.22.1.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/surefire-logger-api/2.22.1/surefire-logger-api-2.22.1.jar (13 kB at 134 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/codehaus/plexus/plexus-utils/1.5.15/plexus-utils-1.5.15.jar
Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/plugin-tools/maven-plugin-annotations/3.5.2/maven-plugin-annotations-3.5.2.jar (14 kB at 121 kB/s)
Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/reporting/maven-reporting-api/3.0/maven-reporting-api-3.0.jar
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Downloading from central: https://repo.maven.apache.org/maven2/org/apache/maven/maven-toolchain/2.2.1/maven-toolchain-2.2.1.jar
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Downloading from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M8/qdox-2.0-M8.jar
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Downloaded from central: https://repo.maven.apache.org/maven2/org/apache/maven/surefire/maven-surefire-common/2.22.1/maven-surefire-common-2.22.1.jar (528 kB at 1.4 MB/s)
Downloaded from central: https://repo.maven.apache.org/maven2/com/thoughtworks/qdox/qdox/2.0-M8/qdox-2.0-M8.jar (316 kB at 682 kB/s)
[INFO] ------------------------------------------------------------------------
[INFO] BUILD FAILURE
[INFO] ------------------------------------------------------------------------
[INFO] Total time:  02:51 min
[INFO] Finished at: 2020-01-31T13:54:53+01:00
[INFO] ------------------------------------------------------------------------
[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.22.1:test (default-test) on project artemis: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.22.1:test failed: Plugin org.apache.maven.plugins:maven-surefire-plugin:2.22.1 or one of its dependencies could not be resolved: Could not transfer artifact org.apache.maven.surefire:surefire-booter:jar:2.22.1 from/to central (https://repo.maven.apache.org/maven2): Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.120.215] failed: Connection timed out (Connection timed out) -> [Help 1]
[ERROR] 
[ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
[ERROR] Re-run Maven using the -X switch to enable full debug logging.
[ERROR] 
[ERROR] For more information about the errors and possible solutions, please read the following articles:
[ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/PluginResolutionException
kpepper commented 4 years ago

Looks like the connection to the maven repo timed out - may be a network issue I would guess..

Connect to repo.maven.apache.org:443 [repo.maven.apache.org/151.101.120.215] failed: Connection timed out (Connection timed out) -> [Help 1]

lalalagartija commented 4 years ago

Thank you ! After several tries it finally worked !